Pyramids, seeking their first-ever continental title, will host the return leg in Cairo on Friday with a place in the final at stake.
Despite playing away, the Egyptian side dominated for large spells and saw two goals disallowed after VAR reviews.
Goalkeeper Ahmed El-Shennawy was called into action early, parrying a long-range effort from Pirates winger Mohau Nkota in the 10th minute.
Pyramids thought they had taken the lead just before halftime when Fiston Mayele found the net, but the Congolese striker was ruled offside following a VAR check.
El-Shennawy produced another crucial save in the 56th minute, denying Patrick Maswanganyi’s left-footed shot from outside the area.
Mostafa Fathi squandered a golden opportunity on the counter when he fired over the bar despite being unmarked.
Moments later, Mayele missed again with a close-range header that sailed over the crossbar.
Pyramids continued to press in the final stages, with substitute Sodiq Awujoola heading home what appeared to be the winner five minutes from time.
However, the goal was disallowed after VAR detected a handball in the buildup.
Pyramids FC reached the semi-finals for the first time in the club’s history after edging Morocco’s FAR Rabat 4-3 on aggregate.
Pirates advanced with a narrow 1-0 aggregate win over Algeria’s MC Alger.
Earlier on Saturday, defending champions Ahly were also held to a 0-0 draw away to Mamelodi Sundowns in the first leg of the other semi-final, keeping their bid for a third consecutive title and record-extending 13th alive ahead of next week’s second leg in Cairo.
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